Your .cif file likely has invalid data.  For instance there are author assigned and reference chain ids in mmcif and perhaps one of those variants is mangled in what Coot wrote.  We will not be able to help unless you provide the file.

Tom


On Dec 1, 2025, at 12:59 PM, Abhilash Padavannil via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi All,

I am having trouble with .cif files in Chimerax — I re-built the model (Model-Angelo) in coot using alpha-fold models for completion and saved it as a .cif file. When I open the file in Chimerax certain proteins in the complex show up differently and the their chain IDs are missing in the Chimerax list. Could you help me fix this ?

Previously I was able to combine the individual alpha-fold models to a single  in Chimerax .cif file. However, if I do local refinement in coot the chains go back to being different. Please suggest. Attached is the screen shot for reference.

Thank you.

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